Arginine Decarboxylase expression, polyamines biosynthesis and reactive oxygen species during organogenic nodule formation in hop

Fortes, Ana Margarida; Costa, Joana C.; Santos, Filipa C.; Seguí-Simarro, José M.; Palme, Klaus; Altabella, Teresa; Tiburcio, Antonio F.; Pais, M. S.

doi:10.4161/psb.6.2.14503

Cited by 21 publications

(10 citation statements)

References 48 publications

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“…Most modules can be partially supported by the potential interactions among the predicted TFs within these modules predicted by STRING or by the possible match between the DNA binding motifs of the putative TFs and the conserved motifs in the upstream sequences of the genes in the modules. Some relationships between the nodulation development and the gene function of modules based on biological experiments were reported in the previous work [ 41 , 46 - 51 ].…”

Section: Resultsmentioning

confidence: 99%

Predicting gene regulatory networks of soybean nodulation from RNA-Seq transcriptome data

et al. 2013

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BackgroundHigh-throughput RNA sequencing (RNA-Seq) is a revolutionary technique to study the transcriptome of a cell under various conditions at a systems level. Despite the wide application of RNA-Seq techniques to generate experimental data in the last few years, few computational methods are available to analyze this huge amount of transcription data. The computational methods for constructing gene regulatory networks from RNA-Seq expression data of hundreds or even thousands of genes are particularly lacking and urgently needed.ResultsWe developed an automated bioinformatics method to predict gene regulatory networks from the quantitative expression values of differentially expressed genes based on RNA-Seq transcriptome data of a cell in different stages and conditions, integrating transcriptional, genomic and gene function data. We applied the method to the RNA-Seq transcriptome data generated for soybean root hair cells in three different development stages of nodulation after rhizobium infection. The method predicted a soybean nodulation-related gene regulatory network consisting of 10 regulatory modules common for all three stages, and 24, 49 and 70 modules separately for the first, second and third stage, each containing both a group of co-expressed genes and several transcription factors collaboratively controlling their expression under different conditions. 8 of 10 common regulatory modules were validated by at least two kinds of validations, such as independent DNA binding motif analysis, gene function enrichment test, and previous experimental data in the literature.ConclusionsWe developed a computational method to reliably reconstruct gene regulatory networks from RNA-Seq transcriptome data. The method can generate valuable hypotheses for interpreting biological data and designing biological experiments such as ChIP-Seq, RNA interference, and yeast two hybrid experiments.

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Section: Resultsmentioning

confidence: 99%

Predicting gene regulatory networks of soybean nodulation from RNA-Seq transcriptome data

et al. 2013

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“…This is well illustrated by experiments that use of scavenger of ROS resulting in the impairment of hop nodule formation and indeterminate nodule formation [51, 116]. Thus, the tight control of when, where, and to what levels ROS/RNS are present might be pivotal to trigger morphogenic events.…”

Section: Common Features In Diverse Morphogenic Processesmentioning

confidence: 96%

“…Reactive oxygen species were shown to accumulate at a necrotic cell layer that marks the future region of nodule separation [ 50 , 51 ]. Hydrogen peroxide which accumulates in nodular cells may act as a signalling molecule-regulating development and programmed cell death [ 52 ].…”

Section: Role Of Stress-induced Enzymes and Derivative Productsmentioning

confidence: 99%

“…During organogenic nodule formation in hop, two isoforms of ADC were detected [ 51 ]. The increase in the levels of two ADC isoenzymes with the concomitant decrease in arginine levels during prenodular and nodular formation were related to increased polyamine synthesis and their role in morphogenesis [ 23 , 51 ]. In accordance, polyamines have been related to the formation and development of globular embryos and organogenesis [ 64 , 66 ].…”

Section: Growth Regulatorsmentioning

confidence: 99%

“…Similarly, oxidative burst, in form of H 2 O 2 and oxygen singlet, has been detected during the infection by the symbionts and later in infected cells of young nodules for nodule formation [ 115 ]. Comparatively, the oxidation of nitro blue tetrazolium due to presence of ROS could be detected around wounded areas of the explant and further on at nodule separation into “daughter nodules” ( Figure 3 [ 51 ]).…”

Section: Common Features In Diverse Morphogenic Processesmentioning

confidence: 99%

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Organogenic Nodule Formation in Hop: A Tool to Study Morphogenesis in Plants with Biotechnological and Medicinal Applications

Fortes

Santos

Pais

2010

Journal of Biomedicine and Biotechnology

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The usage of Humulus lupulus for brewing increased the demand for high-quality plant material. Simultaneously, hop has been used in traditional medicine and recently recognized with anticancer and anti-infective properties. Tissue culture techniques have been reported for a wide range of species, and open the prospect for propagation of disease-free, genetically uniform and massive amounts of plants in vitro. Moreover, the development of large-scale culture methods using bioreactors enables the industrial production of secondary metabolites. Reliable and efficient tissue culture protocol for shoot regeneration through organogenic nodule formation was established for hop. The present review describes the histological, and biochemical changes occurring during this morphogenic process, together with an analysis of transcriptional and metabolic profiles. We also discuss the existence of common molecular factors among three different morphogenic processes: organogenic nodules and somatic embryogenesis, which strictly speaking depend exclusively on intrinsic developmental reprogramming, and legume nitrogen-fixing root nodules, which arises in response to symbiosis. The review of the key factors that participate in hop nodule organogenesis and the comparison with other morphogenic processes may have merit as a study presenting recent advances in complex molecular networks occurring during morphogenesis and together, these provide a rich framework for biotechnology applications.

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Procedures for ADC Immunoblotting and Immunolocalization for Transmission Electron Microscopy During Organogenic Nodule Formation in Hop

Fortes

Seguí-Simarro

2017

Methods in Molecular Biology

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Immunolocalization for transmission electron microscopy is a powerful technique to identify subcellular localization of proteins. This can be combined with molecular and physiological data in order to have a complete overview of protein function. However, optimal sample preservation is required to avoid artefacts. When using chemically fixed samples, the progressive lowering of temperature (PLT) technique is a convenient procedure to dehydrate and embed samples at low temperature, thereby preserving the antigenicity of the proteins to be detected. Despite the advantages of immunogold labelling, it is a time-consuming cell biology technique. Therefore, the quality and specificity of the antibody should be previously checked by western blot. This approach also enables to identify changes in the amount of protein under study throughout development or in response to stress conditions.

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Arginine Decarboxylase expression, polyamines biosynthesis and reactive oxygen species during organogenic nodule formation in hop

Cited by 21 publications

References 48 publications

Predicting gene regulatory networks of soybean nodulation from RNA-Seq transcriptome data

Predicting gene regulatory networks of soybean nodulation from RNA-Seq transcriptome data

Organogenic Nodule Formation in Hop: A Tool to Study Morphogenesis in Plants with Biotechnological and Medicinal Applications

Procedures for ADC Immunoblotting and Immunolocalization for Transmission Electron Microscopy During Organogenic Nodule Formation in Hop

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